Australia are second, one point behind Jordan, with four wins from five matches and three games to go in the second round.
The eight group winners and four best runners-up advance to the third round, which will eventually decide the four automatic qualifiers for Russia in 2018.
The Socceroos opened the scoring in the 40th minute when captain Mile Jedinak converted from the spot after Nathan Burns was brought down heavily inside the box.
Tim Cahill, Australia's all-time leading scorer, doubled the home team's lead five minutes into the second half when he latched onto a perfectly-timed pass from Aaron Mooy.
The impressive Mooy was also instrumental in Australia's third goal, delivering a corner that Kyrgyzstan forward Ildar Amirov misdirected into his own net after 68 minutes.
The reigning Asian champions created more clear scoring opportunities in the final 20 minutes but were unable to extend their advantage through some poor finishing.
"We had a game plan, the boys stuck to it, and maybe we could have been a little bit more (ahead) at the end," Jedinak said in a post-match interview.
"But we'll take the victory and the three points, most importantly."
Australia's next match is away to Bangladesh on Tuesday while Kyrgyzstan are home to Jordan.
(Reporting by Julian Linden in Singapore; Editing by John O'Brien)
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